With ongoing climate change, rising ocean temperature is usually accompanied by falling oxygen levels (hypoxia) and increasing CO2 concentration (hypercapnia). Both drivers may impose constraints on physiological mechanisms that define thermal limits resulting in increased vulnerability towards warming in marine ectotherms. The present study aimed to detect differences in thermal tolerance by investigating the underlying metabolic responses in the green abalone (Haliotis fulgens) under conditions of hypoxia and hypercapnia. Juvenile abalones were exposed to a temperature ramp (+ 3 °C day− 1) under hypoxia (50% air saturation) and hypercapnia (~ 1000 μatm pCO2), both individually and in combination. Impacts on energy metabolism were assessed by analyzing whole animal respiration rates and metabolic profiles of gills and hepatopancreas via 1H NMR spectroscopy. While hypercapnia had a minor impact on the results of the temperature treatment, hypoxia strongly increased the vulnerability to warming, indicated by respiration rates falling below values expected from an exponential increase and by the onset of anaerobic metabolism suggesting a downward shift of the upper critical temperature. Warming under combined hypoxia and hypercapnia elicited a severe change in metabolism involving a strong accumulation of amino acids, osmolytes and anaerobic end products at intermediate temperatures, followed by declining concentrations at warmer temperatures. This matched the limited capacity to increase metabolic rate, loss of attachment and mortality observed under these conditions suggesting a strong narrowing of the thermal window. In all cases, the accumulation of free amino acids identified proteins as a significant energy source during warming stress.